Hi Kipper, Thanks so much, that worked perfectly! Norm From: Kipper Fletez-Brant [mailto:cafletezbrant@gmail.com] Sent: Tuesday, February 25, 2014 12:05 PM To: Norm Allaire Cc: bioconductor@r-project.org Subject: Re: [BioC] creating a qPCRset from Fluidigm 96*96 arrays in HTqPCR Hi Norm, Try re-running your code as follows: temp <- readCtData(exFiles, path = exPath, n.features = 96 * 96, flag = 9, feature =5, type = 6, Ct =7, position= 1, skip=12, sep=",") You didn't have an '=' between skip and 12, so R didn't know how to process your input. Best, Kipper Fletez-Brant On Tue, Feb 25, 2014 at 11:58 AM, Norm Allaire <norm.allaire@biogenidec.com<mailto:norm.allaire@biogenidec.com>> wrote: Hi, I'm new to R. I'm trying to analyze 8 Fluidgm 96 *96 plates (96 assays and 192 samples replicated 4 times). I downloaded and installed HTqPCR and I'm now trying to read in the raw data. I am using the "HTqPCR -high-throughput qPCR analysis in R and Bioconductor" April 14, 2011 as a guide but the example in section 13 is for 48*48 arrays. I tried to modify the 48*48 example to make it work with my files but it doesn't seem to work, I get the following error: > temp <- readCtData(exFiles, path = exPath, n.features = 96 * 96, flag = 9, feature =5, type = 6, Ct =7, position= 1, skip 12, sep=",") Error: unexpected numeric constant in "temp <- readCtData(exFiles, path = exPath, n.features = 96 * 96, flag = 9, feature =5, type = 6, Ct =7, position= 1, skip 12" Any thoughts or suggestions would be greatly appreciated! Norm Allaire Scientist II Genetics and Genomics Biogen Idec 14 Cambridge Center Cambridge, MA 02142 Office: 617-679-2932 e-mail: norm.allaire@biogenidec.com<mailto:norm.allaire@biogenidec.co m=""><mailto:norm.allaire@biogenidec.com<mailto:norm.allaire@biogenidec.c om="">> [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto:bioconductor@r-project.org> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]